Trees | Indices | Help |
---|
|
718 25 26 dbname_conversions = { 27 "bioformat": BioformatDBName(), 28 "unknown": UnknownDBName(), 29 "sp": {"AARHUS/GHENT-2DPAGE": "x-aarhus-ghent-2dpage", 30 "CARBBANK": "x-carbbank", 31 "DICTYDB": "x-dictydb", 32 "ECO2DBASE": "x-eco2dbase", 33 "ECOGENE": "x-ecogene", 34 "EMBL": "embl", # EMBL (in GO) 35 "FLYBASE": "fb", # Flybase (in GO) 36 "GCRDB": "x-gcrdb", 37 "HIV": "x-hiv", 38 "HSC-2DPAGE": "x-hsc", 39 "HSSP": "x-hssp", 40 "MAIZE-2DPAGE": "x-maize", 41 "MAIZEDB": "x-maizedb", 42 "MENDEL": "x-mendel", 43 "MGD": "mgd", # (in GO) 44 "MIM": "x-mim", 45 "PDB": "x-pdb", # Protein Data Bank 46 "PFAM": "x-pfam", 47 "PIR": "pir", # GO 48 "PROSITE": "x-prosite", 49 "REBASE": "x-rebase", 50 "SGD": "sgd", # GO 51 "STYGENE": "x-stygene", 52 "SUBTILIST": "x-subtilist", 53 "SWISS-2DPAGE": "x-swiss", 54 "TIGR": "tigr", # GO 55 "TRANSFAC": "x-transfac", 56 "WORMPEP": "x-wormpep", 57 "YEPD": "x-yepd", 58 "ZFIN": "x-zfin", 59 }, 60 "go": {"CGEN": "cgen", # Compugen, Inc. 61 "DDB": "ddb", # DictyBase (Dictyostelium discoideum) 62 "DDBJ": "ddbj", # DNA Database of Japan 63 "EC": "ec", # Enzyme Commission 64 "EMBL": "embl", # EMBL Nucleotide Sequence Data Library 65 "ENSEMBL": "ensembl", # ENSEMBL 66 "ENZYME": "enzyme", # ENZYME 67 "FB": "fb", # FlyBase 68 "GB": "gb", # GenBank 69 "GO": "go", # Gene Ontology 70 "GXD": "gxd", # Gene Expression Database (mouse) 71 "IPR": "ipr", # InterPro 72 "ISBN": "isbn", # International Standard Book Number 73 "IUBMB": "iubmb", # International Union of Biochemistry 74 # and Molecular Biology 75 "IUPAC": "iupac", # International Union of Pure and Applied 76 # Chemistry 77 "MEDLINE": "medline", # MEDLINE 78 "MGD": "mgd", # Mouse Genome Database 79 "MGI": "mgi", # Mouse Genome Informatics 80 "NC-IUBMB": "NC-IUBMB", 81 # Nomenclature Committee of the International 82 # Union of Biochemistry and Molecular Biology 83 "PIR": "pir", # PIR 84 "PMID": "pmid", # PubMed 85 "Pombase": "pombase", # Schizosaccharomyces pombe 86 "Pompep": "pompep", # Schizosaccharomyces pombe Protein 87 # Sequence Database 88 "RESID": "resid", # RESID (protein post-translational modifications) 89 "SGD": "sgd", # Saccharomyces Genome Database 90 "SP": "sp", # SWISS-PROT 91 "SWALL": "swall", # SWISS-PROT + TrEMBL + TrEMBLnew 92 "TAIR": "tair", # The Arabidopsis Information Resource 93 "taxonID": "taxonid", # Taxonomy ID 94 "TC": "tc", # Transport Commission 95 "TIGR": "tigr", # The Institute of Genome Research 96 "TR": "tr", # TrEMBL 97 "WB": "wb", # WormBase (Caenorhabditis elegans) 98 }, 99 # http://www.ncbi.nlm.nih.gov/collab/db_xref.html 100 "genbank": { 101 "ATCC": "x-atcc", # American Type Culture Collection database 102 # /db_xref="ATCC:123456" 103 "ATCC(in host)": "x-atcc-host", # See above 104 "ATCC(dna)": "x-atcc-dna", # See above 105 106 "BDGP_EST": "x-bdgp-est", # Berkeley Drosophila Genome Project 107 # EST database 108 # /db_xref="BDGP_EST:123456" 109 110 "BDGP_INS": "x-bdgp-ins", # Berkeley Drosophila Genome Project 111 # database -- Insertion 112 # /db_xref="BDGP_INS:123456" 113 114 115 "dbEST": "x-dbest", # EST database maintained at the NCBI. 116 # /db_xref="dbEST:123456" 117 118 "dbSNP": "x-dbsnp", # Variation database maintained at the NCBI. 119 # /db_xref="dbSNP:4647" 120 121 "dbSTS": "x-dbsts", # STS database maintained at the NCBI. 122 # /db_xref="dbSTS:456789" 123 124 "ENSEMBL": "ensembl", # Database of automatically annotated genomic data 125 # /db_xref="ENSEMBL:HUMAN-Clone-AC005612" 126 # /db_xref="ENSEMBL:HUMAN-Gene-ENSG00000007102" 127 128 "ESTLIB": "x-estlib", # EBI's EST library identifier #' 129 # /db_xref="ESTLIB:1200" 130 131 "FANTOM_DB": "x-fantom-db", # Database of Functional Annotation of Mouse 132 # /db_xref="FANTOM_DB:0610005A07" 133 134 "FLYBASE": "fb", # Database of Genetic and molecular data of Drosophila. 135 # /db_xref="FLYBASE:FBgn0000024" 136 137 "GDB": "x-gdb", # Human Genome Database accession numbers. 138 # /db_xref="GDB:G00-128-600" 139 140 "GI": "x-gi", # GenInfo identifier, used as a unique sequence 141 # identifier for nucleotide and proteins. 142 # /db_xref="GI:1234567890" 143 144 "GO": "go", # Gene Ontology Database identifier 145 # /db_xref="GO:123" 146 147 "IMGT/LIGM": "x-imgt-ligm", # Immunogenetics database, immunoglobulins 148 # and T-cell receptors 149 # /db_xref="IMGT/LIGM:U03895" 150 151 "IMGT/HLA": "x-imgt-hla", # Immunogenetics database, human MHC 152 # /db_xref="IMGT/HLA:HLA00031" 153 154 155 "LocusID": "x-locus-id", # NCBI LocusLink ID. 156 # /db_xref="LocusID:51199" 157 158 "MaizeDB": "x-maizedb", # Maize Genome Database unique identifiers. 159 # /db_xref="MaizeDB:Probe/79847" 160 161 "MGD": "mgd", # Mouse Genome Database accession numbers. 162 # /db_xref="MGD:123456" 163 164 "MGI": "mgi", # Medicago Genome Initiative 165 # /db_xref="MGI:S:20819" 166 167 "MIM": "x-mim", # Mendelian Inheritance in Man numbers. 168 # /db_xref="MIM:123456" 169 170 "niaEST": "x-niaEST", # NIA Mouse cDNA Project 171 # /db_xref="niaEST:L0304H12-3" 172 173 "PIR": "pir", # Protein Information Resource accession numbers. 174 # /db_xref="PIR:S12345" 175 176 "PSEUDO": "x-pseudo-embl", # EMBL pseudo protein identifier 177 # /db_xref="PSEUDO:CAC44644.1" 178 179 "RATMAP": "x-ratmap", # Rat Genome Database 180 # /db_xref="RATMAP:5" 181 182 "RiceGenes": "x-ricegenes", # Rice database accession numbers. 183 # /db_xref="RiceGenes:AA231856" 184 185 "REMTREMBL": "x-remtrembl", 186 # Computer-annotated protein sequence database containing 187 # the translations of those codings sequences (CDS) present 188 # in the EMBL Nucleotide Sequence Database that won't be ' 189 # included in SWISS-PROT. These include: immunoglobulins and 190 # T-cell receptors, synthetic sequences, patent application 191 # sequences, small fragments, CDS not coding for real 192 # proteins and truncated proteins. 193 # example: /db_xref="REMTREMBL:CAC01666" 194 195 "RZPD": "x-rzpd", # Resource Centre Primary Database Clone Identifiers 196 # /db_xref="RZPD:IMAGp998I142450Q6" 197 198 "SGD": "sgd", # Saccharomyces Genome Database accession numbers. 199 # /db_xref="SGD:L0000470" 200 201 "SoyBase": "x-soybase", # Glycine max Genome Database 202 # /db_xref="SoyBase:Satt005" 203 204 "SPTREMBL": "x-sptrembl", # is this the same as "swall" ? 205 # Computer-annotated protein sequence database 206 # supplementing SWISS-PROT and containing the 207 # translations of all coding sequences (CDS) 208 # present in the EMBL Nucleotide Sequence 209 # Database not yet integrated in SWISS-PROT. 210 # /db_xref="SPTREMBL:Q00177" 211 212 "SWISS-PROT": "sp", # Swiss-Prot protein database accession numbers. 213 # /db_xref="SWISS-PROT:P12345" 214 215 "taxon": "taxonid", # NCBI taxonomic identifier. 216 # /db_xref="taxon:4932" 217 }, 218 } 2199 if self.reftype is None: 10 reftype = "" 11 else: 12 reftype = self.reftype + "=" 13 s = "%s/%s%s" % (self.dbname, reftype, self.dbid) 14 if self.negate: 15 s = "not(%s)" % s 16 return s17 __repr__ = __str__221 try: 222 dbname = dbname_conversions[dbname_style][dbname] 223 except KeyError: 224 dbname = "x-unknown2-%s--%s" % (dbname_style, dbname) 225 return DBXRef(dbname, dbid, idtype, negate)226
Trees | Indices | Help |
---|
Generated by Epydoc 3.0.1 on Mon Sep 15 09:24:28 2008 | http://epydoc.sourceforge.net |